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MCAT 2015 Biology > Biology - Chapter 4 - Molecular Biology > Flashcards

Biology - Chapter 4 - Molecular Biology Flashcards

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1
Q

DNA stands for ____________

A

Deoxyribonucleic Acid

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2
Q

RNA stands for ___

A

Ribonucleic Acid

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3
Q

Why are DNA and RNA called nucleic acids?

A

because they are found in the nucleus and possess many acidic phosphate groups.

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4
Q

What is the building block of DNA?

A

the building block of DNA is the deoxyribonucleoside 5’ triphosphate - dNTP

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5
Q

What are the three components that build deoxyribonucleotides?

A
  • A simple monosaccharide, ribose (the 2’ OH is missing, so it is a deoxyribose)
  • an aromatic nitrogenous base namely - adenine, guanine, cytosine or thymine

-

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6
Q

Why are the aromatic molecules bases? ( A, T , C, G )

A

because they contain several nitrogens which have free electron pairs capable of accepting protons.

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7
Q

G and A are derived from a precursor called _____

A

purine

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8
Q

Pyrimidines are

A

C and T

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9
Q

Nucleoside

A

A nucleoside is a ribose with a purine or pyrimidine linked to the 1’ carbon in a B-N-glycosidic linkage

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10
Q

The nucleosides

A 
A-ribose = adenosine
G-ribose = guanosine
C-ribose = cytidine
T-ribose = thymidine
U-ribose = uridine
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11
Q

What bonding potentials does purines and pyrimidines have?

A

both purines and pyrimidines have abundant hydrogen bonding potential.

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12
Q

Will adenine and thymine H-bond with each other in dilute aqueous solution (0.1M)

A

No. In dilute solution, they will be H-bonded to water. However, H-bonds are the key determinant of the double-strandedstructure of DNA; in DNA the bases do not interact with water because DNA coiling places them inside the tube-like structure of the double helix, where they interact with each other.

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13
Q

What are nucleotides?

A

Nucleotides are phosphate esters of nucleosides, with one, two, or three phosphate groups joined to the ribose ring by the 5” hydroxy group.

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14
Q

dNTP

A

deoxy
nucleoside
triphosphate

N is replaced by A, G, C, T or U

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15
Q

name ending with “ylate”

A

Because they contain acidic phosphates, the nucleotides may also be referred to by a name ending in “ylate”

eg. TTP is thymidylate

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16
Q

ATP

A

is a nucleotide which may be called adenylate

( its not deoxy)

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17
Q

Which portion of the nucleotide is referred to as the backbone of the DNA?

A

ribose + phosphate portion

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18
Q

Is the backbone in a DNA the same regardless of the nucleotide sequence?

A

yes

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19
Q

Nucleotides in the DNA are covalently linked by _______ bonds

A

Phosphodiester bonds

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20
Q

How are the polynucleotides written?

A

The end of the chain with a free 5” phosphate group is written first in a polynucleotide, with other nucleotides in the chain indicated in the 5” to 3” direction

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21
Q

Which of the nucleotides in the oligonucleotide ACGT has a free 3” hydroxy group?

A

the T is written last and is therefore the 3” nucleotide, or the nucleotide with the free 3” hydroxy group

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22
Q

According to watson-crick model, cellular DNA is a _______ double helix held together by _____ bonds between _____

A

According to watson-crick model, cellular DNA is a right-handed double helix held together by hydrogen bonds between bases.

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23
Q

Two very long polypeptide chains are _________ in the double stranded DNA in antiparallel direction

A

Two very long polypeptide chains are hydrogen bonded in the double stranded DNA in antiparallel direction

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24
Q

What common protein structure depends on H-bonds between antiparallel chains?

A

antiparallel H-bonding is reminiscent of the B-pleated sheet, which is a common secondary structure ( it can be quaternary, when two separate chains come together to form a sheet)

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25
Q

The GC pair is held together by ______ hydrogen bonds

A

three

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26
Q

The AT pair is held together by ______ hydrogen bonds

A

two

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27
Q

ds - DNA 100 nucleotides long……. what does it mean?

A

we would say it is 100 base pairs (bp) long

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28
Q

kbp = kilobase pair

A

ds- DNA 1000 nucleotides long

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29
Q

Annealing

A

The binding of two complementary strands of DNA into a double-stranded structure is termed annealing or hybridization

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30
Q

melting or denaturation

A

The separation of strands is termed melting or denaturation

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31
Q

Tm

A

The temperature at which a solution of DNA molecules is 50% melted

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32
Q

Ratio of purines to pyrimidines ____

A

is always the same … 50:50

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33
Q

where are the bases in the DNA located

A

in the interior.

ribose-phosphate backbone on the exterior

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34
Q

How can a base be hydrophobic?

A

Once a purine is H-bonded to a pyrimidine, most of the polar nature of the individual bases disappears because the charge dipoles are occupied in H-bonds.

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35
Q

the width of the DNA double helix is ALWAYS

A

20Å

Å = angstroms

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36
Q

one angstrom is

A

10^-10 meter

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37
Q

One base pair is _______ meters long

A

3.4 x 10^-10

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38
Q

Genome

A

The sum total of an organism’s genetic information is called its genome.

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39
Q

Prokaryotic (bacterial) genomes are composed of a ______

A

single circular chromosome

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40
Q

Organisms wit the largest known genomes are ______

A

amphibians

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41
Q

How does prokaryotes make their single circular chromosome more compact and sturdy?

A

An enzyme called DNA gyros uses the energy of ATP to twist the gigantic circular molecule.

42
Q

How does gyros function?

A

Gyros function by breaking the DNA and twisting the two sides of the circle around each other. The resulting structure is a twisted circle that is composed of ds-DNA.

43
Q

supercoils

A

The twists created by DNA gyros is called supercoils, since they are coils of a structure that is already coiled.

44
Q

eukaryotes have more ___ in their genome than prokaryotes

A

eukaryotes have more DNA in their genome than prokaryotes

45
Q

histones

A

globular proteins, around which DNA is wrapped around in eukaryotes.

46
Q

Chromatin

A

fully packed DNA is called chromatin.

it is composed of closely stacked nucleosomes.

47
Q

Flow chart summarizing the structure of DNA in the nucleus

A

Deoxyribose —-> Add base —->nucleoside —->add three phosphates —->nucleotide —->polymerize with loss of two phosphates —-> oligonucleotide —-> continue polymerization —-> single stranded polynucleotide —->two complete chains H- bond in antiparallel orientation —-> ds DNA chain —-> coiling occurs —-> ds helix —-> wrap around histones —-> nucleosomes —-> complete packaging —-> chromatin

48
Q

Condensed metaphase chromosomes are _____

A

compact and easier to see.

49
Q

The darker regions of the chromosomes are denser and are called _____

A

heterochromatin

50
Q

The lighter regions of the chromosomes are less dense and are called _____

A

euchromatin

51
Q

the lighter regions of the chromosomes have _____

A

higher transcription rates and therefore higher gene activity.

52
Q

What staring can be used to stain a chromosome?

A

Giemsa stain

53
Q

Centromeres

A

spindle file attach to it during cell division.

the fibres attach via kinetochores

54
Q

What are centromeres made of?

A

they are made of heterochromatin, and repetitive DNA sequence.

55
Q

P arm

A

short arm of chromosome

56
Q

q arm

A

long arm of chromosome

57
Q

Telomeres

A

THE END OF LINEAR CHROMOSOMES ARE CALLED TELOMERES

58
Q

function of telomeres

A

Telomeres function to prevent chromosome deterioration and also prevent fusion with neighbouring chromosomes.

They function as disposable buffers, blocking the ends of chromosomes.

59
Q

Does the DNA of prokaryotes contain telomeres?

A

since most prokaryotes have circular genomes, their DNA does not contain telomeres.

60
Q

Human genome contains

A

24 different chromosomes (22 autosomes plus 2 sex chromosomes)

3.2 billion base pairs

and codes for about 21000 genes

61
Q

intergenic regions

A

are composed of noncoding DNA.

These regions may direct the assembly of specific chromatin structures, and can contribute to the regulation of nearby genes, but many have no known function.

62
Q

What is a gene?

A

A gene is a DNA sequence that encodes a gene product.

It includes both promoters and transcription stop sites and a region that codes for either a protein or a non-coding RNA.

63
Q

Single nucleotide polymorphisms

A

they are essentially mutations.

known as SNPs

it describes the fact that the nucleotide sequence in the human genome changes ever 1000 base pairs randomly.

64
Q

where do SNPs mostly occur?

A

in the non coding regions of the genome.

65
Q

CNVs

A

Copy Number Variation

Changes apply to much larger regions of the genome compared to SNPs.

CNVs are normal part of our genome (0.4% of the genome can have CNV)

66
Q

Copy number variation

A

CNVs are structural variations in the genome that lead to different copies of DNA sections.

67
Q

What does the DNA contain essentially?

A

The DNA contains sequences of nucleotides known as genes that serve as templates for the production of another nucleic acid known as RNA.

68
Q

Transcription

A

The process of reading the DNA and writing the information as RNA is termed transcription.

It can generate -

  1. either a final gene product ( e.g.. all non coding RNAs),

or

  1. A messenger molecule
69
Q

Translation

A

The synthesis of proteins using RNA as template is termed translation.

70
Q

DNA ——-> ________ ——-> protein

A

DNA ——-> RNA ——-> Protein

This unidirectional flow equation represents the central dogma of molecular biology.

71
Q

Genetic Code

A

The language used by DNA and mRNA to specify the building blocks of proteins is known as the Genetic Code.

72
Q

Codon

A

A number of experiments confirmed that the genetic code is written in three-letter words, each of which codes for a particular amino acid. A nucleic acid word ( 3 nucleotide letters) is referred to as a codon.

73
Q

DNA to RNA….. Same language?

A

Cellular transcription is a process whereby a code is read from a nucleic acid (DNA) and written in the language of another nucleic acid (RNA), so the language is the same.

In cellular translation, nucleic acids are read and polypeptides are written, so here the language does change.

74
Q

RNA has U instead of ____

A

T

75
Q

What does the stop codon do?

A

Notify the ribosome that the protein is complete and cause it to stop reading the mRNA.

76
Q

Stop codons are also called ________

A

Nonsense codons

77
Q

Most of the _____ amino acids can be coded for more than one codon.

A

Most of the 20 amino acids can be coded for more than one codon.

Often all four of the codons with the same first two nucleotides e.g. CU_ encode the same amino acid.

78
Q

Switching the third nucleotide in the majority of codons will ______ effect

A

Switching the third nucleotide in the majority of codons will no effect

79
Q

The __________ is the control centre of the cell

A

The DNA genome is the control centre of the cell

80
Q

Replication

A

duplication of the DNA

81
Q

Krebs cycle, glycolysis, replication are all _______ processes

A

Krebs cycle, glycolysis, replication are all enzymatic processes

82
Q

The old DNA is called ______ DNA

A

The old DNA is called parental DNA

83
Q

conservative replication theory

A

The parental ds-DNA would remain as-is while an entire new double stranded genome is created.

84
Q

dispersive theory of DNA replication

A

The theory sid that both copies of the genomes were composed of scattered pieces of new and old DNA

85
Q

DNA replication is actually __________

A

semiconservative.

After replication, one strand of the new double helix is parental and one strand is newly synthesized daughter DNA

86
Q

Semiconservative replication of DNA

A

Individual strands of the double stranded parent are pulled apart, then a new daughter strand is synthesized using the parental DNA as a template to copy from. Each new daughter chain is perfectly complementary to its template or parent.

87
Q

Helicase

A

The enzyme that unwinds the double helix and separates the strands is called helicase

88
Q

Would you expect helicase to use the energy of ATP hydrolysis to do its job?

A

Yes. Separating the strands requires the breaking of many H-bonds.

89
Q

ORI

Origin of Replication

A

The place where the helicase begins to unwind.

90
Q

In prokaryotes, which protein finds the ORI?

A

a protein called DnaA

91
Q

In eukaryotes, which proteins find the ORI?

A

Three proteins cooperate to find the ORI.

two of them are synthesized during the M and G1 phases of the cell cycle, but are rapidly destroyed as the S phase begins.

92
Q

Which protein protects the DNA that has been unpackaged in preparation for replication and help keep the strands separated?

A

SSBPs

Single Strand Binding Proteins

93
Q

Open complex

A

The separated strands of the DNA are referred to as the open complex

94
Q

DNA Replication

A
  • An RNA primer must be synthesized for each template strand.
  • This is accomplished by a set of proteins called the promise, of which the central component is an RNA polymerase called primase.
  • Primer synthesis is important because the next enzyme, DNA polymerase, cannot start a new DNA chain from scratch. It can only add nucleotides to an existing nucleotide chain.
  • Daughter DNA is created as a growing polymer.
  • DNA polymerase catalyzes the elongation of the daughter strand using the parental template, and elongates the primer by adding dNTPs to its 3’ end.
  • In fact the 3’ hydroxyl group acts as a nucleophile in the polymerization reaction to displace 5’ pyrophosphate from the dNTP to be added.
  • DNA pol is part of a large complex of proteins called the replisome.
95
Q

The template strand is read in what direction?

A

If the daughter is made 5’ to 3’, and the two strands have to end up antiparallel, the template must be read 3’ to 5’

96
Q

Prokaryotic replisome contains ____ components.

eukaryotic replisome contains ____ proteins.

A

13

27

97
Q

What is the thermodynamic driving force for the polymerization reaction?

A

the thermodynamic driving force for the polymerization reaction is the removal and hydrolysis of pyrophosphate from each dNTP added to the chain.

(P207^-4)

98
Q

Replication rules (memorize)

A
  • Polymerization occurs in the 5’ to 3’ direction, WITHOUT EXCEPTION. This means the existing chain is always lengthened by the addition of a nucleotide to the 3’ end of the chain. THERE IS NEVER 3’ TO 5’ POLYMERASE ACTIVITY.
  • DNA POL REQUIRES A TEMPLATE. It can not make a DNA chain from scratch but must copy an old chain.
  • DNA polymerase requires a primer. It cannot start a new nucleotide chain.
  • Replication forks grow away from the origin in both directions. Each replication fork contains a leading strand and a lagging strand.
  • Replication of the leading strand is continuous and leads into the replication fork, while replication of the lagging strand in discontinuous, resulting in okazaki fragments.
  • Eventually all RNA primers are replaced by DNA, and the fragments are joined by an enzyme called DNA ligase.
99
Q

Chain elongation can only proceed in one direction, _______

A

5’ to 3’

100
Q

Leading strands

A

the bottom daughter on the right side

and the top daughter on the left side are called the leading strands.

101
Q

Lagging strand

A

The top daughter on the right, and the bottom daughter on the left are called the lagging strands because they must wait until the replication fork widens before beginning to polymerize.

The small chunks of DNA comprising the lagging strand are called okazaki fragments.

102
Q

As the replication forks grow, does helicase have to continue to unwind the double helix and separate the strands?

A

Yes

MCAT 2015 Biology (3 decks)

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